Contacts of the strand formed by residues 222 - 227 (chain B) in PDB entry 4BVH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 3.8 6.3 - - - +
142B VAL* 3.7 30.1 - - + -
213B LEU* 4.5 8.3 - - + +
216B LEU* 3.8 10.5 + - + -
217B HIS* 3.8 38.5 + - + +
220B GLY 3.7 2.3 - - - -
221B LEU* 1.3 74.5 - - - +
223B LEU* 1.3 58.4 - - - +
224B ARG* 3.7 21.8 - - - +
225B LEU* 4.2 18.4 - - + +
239B ILE* 4.5 9.9 - - + -
243B LYS* 2.9 45.9 + - + -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ARG* 4.0 19.9 - - + +
140B VAL 2.8 19.6 + - - +
141B VAL* 3.7 13.7 - - + -
221B LEU 3.5 3.0 + - - -
222B LEU* 1.3 74.5 - - - +
224B ARG* 1.3 77.7 + - + +
243B LYS* 3.8 15.7 + - - +
308B ASP* 3.6 40.8 - - - +
311B MET* 3.8 28.3 - - + +
312B ALA* 4.1 2.0 - - - +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL 3.7 0.4 + - - -
141B VAL* 3.5 6.3 - - + +
142B VAL 2.9 25.1 + - - +
222B LEU* 3.5 9.4 - - - +
223B LEU* 1.3 97.3 + - + +
225B LEU* 1.3 62.0 + - - +
226B TYR* 3.5 18.8 - - + -
242B SER* 2.8 34.2 + - - -
243B LYS* 3.4 20.7 - - - +
245B VAL* 3.7 19.3 - - + -
301B ARG* 4.2 2.8 - - - +
304B LEU* 4.3 20.0 - - - +
308B ASP* 2.8 48.7 + - + +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL* 3.6 12.1 - - + +
144B VAL* 4.0 12.6 - - + -
213B LEU* 3.9 27.6 - - + -
222B LEU* 4.2 12.8 - - + -
224B ARG* 1.3 73.4 - - - +
226B TYR* 1.3 71.7 + - - +
227B THR* 4.0 10.3 - - - -
234B GLU* 3.7 24.0 - - + -
239B ILE* 4.0 24.0 - - + -
243B LYS 2.8 13.9 + - - +
244B LEU* 3.4 15.3 - - + +
245B VAL 2.8 30.1 + - - -
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Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 4.1 6.5 - - + -
142B VAL 2.8 17.4 + - - +
143B MET* 3.3 5.6 - - + -
144B VAL 3.0 24.4 + - - -
224B ARG* 3.5 16.8 - - + -
225B LEU* 1.3 75.8 - - - +
227B THR* 1.3 60.6 + - - +
245B VAL* 3.6 34.5 - - + -
302B PHE* 4.0 21.3 - + - -
304B LEU* 3.2 5.0 - - - +
305B HIS* 2.9 41.2 + - + -
308B ASP* 2.5 32.0 + - + -
309B PHE* 3.8 19.3 - + - -
327B PHE* 3.6 19.6 - + + -
330B LEU* 4.5 4.3 - - + -
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Residues in contact with THR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL* 3.4 15.5 - - - +
225B LEU* 3.9 2.4 + - - -
226B TYR* 1.3 73.7 - - - +
228B GLN* 1.3 62.7 + - - +
229B ASN* 3.0 23.5 + - - +
234B GLU* 2.7 41.9 + - - +
244B LEU* 4.2 6.5 - - + -
245B VAL 2.9 18.0 + - - +
246B GLU* 3.9 18.4 - - + -
247B ALA* 2.9 29.8 + - - +
248B HIS 3.9 0.3 + - - -
327B PHE* 4.0 2.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il